ancient-dna
There are 38 repositories under ancient-dna topic.
moiexpositoalonsolab/grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
SPAAM-community/AncientMetagenomeDir
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
sneuensc/mapache
mapping pipeline for ancient DNA
bodkan/archaic-ychr
Repository of code for the paper "The evolutionary history of Neandertal and Denisovan Y chromosomes" by Petr et al.
jfy133/Tidy_PopGen_PCA_Plotting
A small R notebook describing how plot common (aDNA) population genetics PCAs using R and the tidyverse.
maxibor/pydamage
Damage parameter estimation for ancient DNA
albanieto/aDNA-analysis
A beginner's guide to aDNA analysis, including scripts to streamline the process.
nf-core/coproid
Coprolite host Identification pipeline
poseidon-framework/community-archive
The Poseidon Community Archive (PCA)
sunyatin/ASCEND
Method to estimate the age and intensity of recent bottlenecks/founder events, using genotype data and a recombination map.
poseidon-framework/poseidon-hs
A toolset to work with modular genotype databases in the Poseidon format
tschuelia/Pandora
Uncertainty estimation toolkit for dimensionality reduction on population genetics data.
mpieva/quicksand
A pipeline for the analysis of sedimentary ancient mtDNA
nevrome/mobest
R Package - Spatiotemporal Ancestry Interpolation and Search
CamilaDuitama/decOM
🗑️🦷 decOM 🦷🗑️
MPI-EVA-Archaeogenetics/ethics_statement
Statement of the Ethics Discussion Group at the Department of Archaeogenetics (MPI-SHH/MPI-EVA)
poseidon-framework/poseidon-framework.github.io
Main landing page for getting information about the Poseidon project
Allaby-lab/PIA
Phylogenetic intersection analysis (PIA) from the Allaby lab, University of Warwick: doi.org/10.3389/fevo.2020.00084
nevrome/mobest.analysis.2022
Research compendium for ‘Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data’; If you want to perform spatio-temporal similary search with the mobest R package as presented in the paper, then you can directly check the documentation here: https://nevrome.de/mobest
paleobiotechnology/EMN001_Paleofuran
Repository for data, code & figures related to the publication: "Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic"
sidora-tools/sidora.core
Backend for all sidora applications
etkayapar/bamRefine
Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog
fj-blanco/bam-to-ychr-calls
From .bam to .csv with annotated Y-chromosome variants
md5sam/aKmerBroom
🧹 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
nevrome/paagen
Experiments with the genotype data generators in xerxes
poseidon-framework/janno
R Package - Handling .janno files in R
SPAAM-community/AMDirT
AncientMetagenomeDir Toolkit
achimklittich/WindowTrees
Program to generate RAxML sliding window trees
Allaby-lab/PIA-accessories
Additional tools for manipulating PIA output.
MaelLefeuvre/grups-rs
An ancient DNA genetic relatedness estimation software relying on pedigree simulations
MaelLefeuvre/grups.plots
grups.plots is a companion R package to grups-rs, providing with a Shiny dashboard, harboring multiple interactive visualizations, utilities and summary statistics to analyse its results
SPAAM-community/ancient-metagenomics-labs
Website and data repository a directory of ancient metagenomic labs
DanielRCA/NCR-mtDNA_ampliconbasedngs
A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods
poseidon-framework/aadr-archive
The Poseidon AADR Archive (PAA)
poseidon-framework/qjanno
A CLI tool to run SQL queries on Poseidon .janno files